Applying to Activate Tencent Healthcare Omics Platform
All the management-related features of the Tencent HealthCare Omics Platform environment can be accessed through the Console. Team administrators can access the environment management page in the console to create, view, and delete environments.
On the environment management page, click Go to Apply to jump to Tencent HealthCare Omics Platform Application page to complete the relevant information (contact information, company name, etc.). After you submit the application, we will complete the review as soon as possible, and the review results will be sent to you via Short Message Service and message center. At the same time, our architect will contact you to provide better service.
Creating a New Environment
Omics Environment Overview
The normal operation of Tencent Healthcare Omics Platform depends on the support of the underlying cloud environment resources (including computing resources such as Tencent Kubernetes Engine, Cloud Object Storage, and Cloud File Storage). After the relevant cloud resources are prepared, Tencent Healthcare Omics Platform can quickly, smoothly, and efficiently help you use the selected Tencent Cloud resources to perform omics-related data analysis. Therefore, before officially starting the analysis task, you need to create a running environment in Tencent Cloud. When performing the analysis task, you can select the suitable environment to run your application as needed.
Omics Environment Selection
Tencent Healthcare Omics Platform provides two types of environments for you: omics Managed Environment and omics standard environment. For selection, see the following table:
Product Selection
Omics Managed Environment
Standard Environment
Features
Fully Serverless
One-Stop Service
Security Sandbox Container
Support node management.
Network Interconnection
Full-Stack Business Scenes Supported
Management Node
No management node fee is charged. Billing is performed based on the actual task running duration.
Management nodes are supported, and computing resources are billed based on the actual task running duration.
Use Cases
Applies to production and computing tasks with high stability, large scale, and elastic peaks.
Supports security sandbox containers and provides a test isolation environment to facilitate development and debugging.
Applies to all business scenarios of bioinformatics analysis.
Supports management nodes, and computing resources are charged based on the actual task running duration.
Network connection between products under the same Tencent Cloud account is supported.
Workflow Engine
Nextflow, WDL, Snakemake
Nextflow, WDL
Batch Submission
Supported
Supported
Cache Management
Refined cache management is supported.
One-click cleaning is supported.
Call Caching
Supported
Supported
Create a new environment
Click Create New Environment and select the appropriate environment type in the pop-up:
1. If you choose to create an omics Managed Environment, you can see the following content to configure the environment parameters:
Environment Name
The environment name cannot contain more than 50 characters.
Region
Currently, you can select clusters in Guangzhou, Shanghai, or Beijing. It is recommended to select a region that is geographically close to you and where the bucket is located to reduce access latency, increase download speed, and avoid cross-region traffic fees.
Select The Default Volume Type
As a computing cache for Tencent Healthcare Omics Platform, you can choose volumes (provide service based on CFS) with different performance according to the analysis scale. There are four types of volumes supported, including the general standard type, general performance type, standard turbo, and high-performance turbo. For the performance, specifications, and features of the four types of file storage, see the documentation in Cache File Management - Cache Volume Performance and Specifications for comparison. When creating an environment, you need to specify the default cache volume type. Then, you can create other volumes as needed.
Default Environment
The default environment is an environment where all users have permission to submit tasks, and all work projects are bound to it by default. For non-default environments, managers need to bind the running environment to the work projects. Then, the corresponding work projects have permission to submit tasks for this environment.
2. If you choose to create a standard omics environment, you can see the following content to configure the environment parameters:
Select Basic Configuration
Environment Name
The environment name cannot contain more than 50 characters.
Region
Currently, you can select clusters in Guangzhou, Shanghai, or Beijing. It is recommended to select a region that is geographically close to you and where the bucket is located to reduce access latency, increase download speed, and avoid cross-region traffic fees.
Availability Zone(AZ)
Based on the region you select, we provide different availability zones in that region for you to choose from. You can view the current list of available availability zones on the Create a New Environment page.
Management Node
To ensure secure and convenient usage of the Tencent HealthCare Omics Platform, when the user creates an omics standard environment, one CVM instance and one omics computing container instance are automatically created under the user's Tencent Cloud account and deployed as management nodes. The management nodes are created and terminated along with the activated standard environment. You do not need to manage them. Specifications and configurations of management nodes are as follows:
Resource Type
Specification
Configuration
Quantities
Reference Fees
CVM
SA3.MEDIUM8
2-core vCPU, 8 GB memory
1
0.35 CNY/hour
Omics Computing
Pod
1-core vCPU, 8 GB memory
1
CPU: 0.12 CNY/core/hour
Memory: 0.05 CNY/GiB/hour
Note:
If you do not use the standard omics environment to submit bioinformatics analysis tasks for a long time, delete and release the standard omics environment in time to prevent unnecessary waste of resources and fees.
Select The Default Volume Type
As a computing cache for Tencent Healthcare Omics Platform, it supports you to choose CFS types with different performances according to the analysis scale. There are four types of CFS supported, including general standard type, general performance type, standard turbo, and high-performance turbo. For the performance, specifications, and features of the four types of CFS, see the documentation in CFS > Storage Types and Performance Specifications for comparison.
If you select a turbo type, a storage capacity selection bar will pop up. The storage capacity selection range for a standard turbo is from 20 TiB to 1,000 TiB, while the storage capacity selection range for a high-performance turbo is from 10 TiB to 500 TiB. Storage capacity selection is mandatory. If you select other types, you do not need to select storage capacity.
Default Environment
The default environment is an environment where all users have permission to submit tasks, and all work projects are bound to it by default. For non-default environments, managers need to bind the running environment to the work projects. Then, the corresponding work projects have permission to submit tasks for this environment.
Environment Descriptions
This field is optional. Users can note the purpose of the environment, related projects, and other information in the environment description.
Set Network, Quota, and Default Settings
VPC: This field displays all VPC networks you have created in the region. Select a suitable network as the private network for this environment. If there is no available network information or the existing network is not suitable, you can jump to the console to create a new private network. For details, see VPC (VPC). The subnet in the Virtual Private Cloud will be used for the container network of the serverless cluster.
Service CIDR: The ClusterIP service of the cluster is allocated to the selected VPC subnet by default. Try to choose a subnet with sufficient IPs and not against the use of other products.
Security Group: The security group has the feature of a firewall. It can limit the network communication of the workload. Configure the network rules necessary for running the security group bound to the workload. If there is no valid security group in the region, you can go to the console to create a security group.
Scheduler: The omics environment provides Kubernetes as a scheduler.
Add Image Access Credential
Container images are private by default. To ensure that your image in the Tencent container image repository can be used normally in Tencent Healthcare Omics Platform environment, you need to add the image access credentials corresponding to the environment and establish the association between the image instance and Tencent Healthcare Omics Platform environment when creating the environment. The steps are as follows:
Step 1
On the environment management page, click the environment name to jump to the environment details page.
Step 2
On the environment details page, click Add Credential in the upper right corner of the image repository access credentials module. A pop-up for adding image access credentials will appear.
Step 3
In the Add Image Access Credentials pop-up, you need to first select the region corresponding to the image instance you want to associate. If the instance list displayed is empty, click Add Image Instance and go to Console > TCR to create the image instance to be associated first. After creation, return to Tencent Healthcare Omics Platform's environment management details page, refresh the list in the pop-up, and then view and select the corresponding image instance.
Note:
An image instance usually contains multiple image repositories, and all image repositories in the same image instance share the same image access credential.
Note:
By default, the region for the image instance is the same as that of the omics computing environment. If you select another region and associate the enterprise image instance, you may incur public network access traffic fees when using it.
The image credential delivery process takes some time. During the delivery process, the image credential is being issued. When the status is updated to "issuing" status, the image credential takes effect.
Update Image Access Credential Configuration
If you delete the access credentials associated with the omics environment in the container image service, you need to update the access credential configuration to ensure that the image under the instance can be used normally. Click the operation option Update Configuration corresponding to the credential to be updated, and the Update Configuration pop-up will appear.
In the Configuration Updating of Access Credential pop-up, enter the instance user name and initialized password or new credential password to complete the configuration update. The credential will be issued next time.
There are two ways to obtain the password used to update the image access credentials: Update credential configuration using the password of the image instance and Update credential configuration using a new instance credential to obtain a new password.
Method 1: Obtain credential configuration using the password of the image instance
1. In the console > TCR page, enter the Instance Management page. On the instance overview page, click option Access TCR instance in the upper right corner of the Instance Overview menu, and a pop-up for instance details will appear.
2. Save the access credential log-in userword and password which can be used to update the access credential configuration.
Method 2: Update credential configuration using a new image access credential to obtain a new password
1. Go to the Console - Tencent Container Registry, select the user-level account in the access credentials column, and the user-level account image access credentials list page is displayed. Click the new option in the upper right corner, and the new credential pop-up is displayed.
2. After creating a new access credential, save the access credential log-in password. The password can be used to update the access credential configuration.
View Environment
View Environment Status
On the environment management page, the environment list is displayed, and the status of each environment can be viewed. There are 5 types of environment status, including Creating (including creating and recreating), Running, Deleting, Abnormal, and Creation failed. Click the exclamation mark icon near Creation Failed to view the error summary.
For environments that are being of Creating, click Detail Inquiry to check the progress of each environment creation process. If the creation fails, hover the mouse pointer over the reason column to display the specific reason for failure.
The details page supports viewing the environment status, container cluster resources, file storage usage/total capacity, and Cloud File Storage throughput upper limit.
Deleting environments is supported.
View Environment Details
On the environment management page, users can view environment details by clicking the corresponding environment ID when encountering environments that are running or in exceptional status.
The environment basic information page displays the environment configuration parameters, cluster type, creation time, and other information.
Deleting an Environment
On the environment management page, click Delete button in the operation column of the environment to be deleted. The Delete environment pop-up will appear. The pop-up contains the resource type, ID, and whether it can be deleted for each resource in the environment. Some resources cannot be deleted. Hover the mouse pointer over Non-deletable to show the reason why the resource cannot be deleted.
If you want to delete an environment, you need to manually enter the resource ID in the ID input box at the bottom of the pop-up. After the confirmation, delete the environment. The environment-related resources will be deleted or disassociated from Tencent Healthcare Omics Platform environment. (Resources of the type "Non-deletable" will be disassociated from Tencent Healthcare Omics Platform environment but will not be deleted. Other types of resources will be deleted.)
Note:
After you create the environment for running Tencent Healthcare Omics Platform in the console, some underlying cloud resources will be consumed to maintain the normal operation of Tencent Healthcare Omics Platform, and there will be related fees. To avoid unnecessary waste, environments that have not been used for a long time need to be deleted in time to release corresponding resources.
Binding Projects to Environments
In the Create a New Project or Project Settings pop-up, you can specify the running environment available for the project by binding the project to the running environment.
Selecting an Environment
On the running settings page for the specific application of the work project (for related operations, see Application), you can select the running environment (single choice), but you cannot select an unavailable environment (grayed out option).
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